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DREAM 7 Challenge Seeks Informatics Solutions to Support Translational Medicine

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The organizers of the annual Dialogue for Reverse Engineering Assessment and Methods have released this year's informatics challenges, which are focused on applications that support translational medicine.

Three of the four challenges for DREAM 7 call for the development of informatics tools and methods that will support ongoing efforts to treat cancer and amyotrophic lateral sclerosis.

Full details of all four challenges and their associated datasets will be made available on the DREAM website within the next few weeks.

Speaking with BioInform this week, Pablo Meyer, a post-doctoral fellow at IBM Research and one of the DREAM 7 organizers, noted that while DREAM initially had a more academic focus, it has evolved to become "a community of people that go beyond solving just academic challenges."

"This year ... is a good example of [challenges] that [are] more applied," he said.

Commenting on this year's focus on disease applications, Gustavo Stolovitzky, manager of functional genomics and systems biology at IBM and a DREAM founder, explained that the contest has grown since its launch seven years ago to become "a very serious channel to do crowdsourcing [in] systems biology."

DREAM's approach allows the systems biology community to take advantage of "the wisdom of crowds" and get a better understanding of research problems, which is the "real interesting part," he told BioInform.

For example, aggregating the best results from teams in each of the categories from previous challenges has resulted in improved methods and better results. "We have verified this in challenge after challenge," he said.

For this year's challenges, the DREAM organizers are partnering with the National Cancer Institute, Sage Bionetworks, and Prize4Life, a not-for-profit organization that supports efforts to discover treatments for ALS.

The first challenge, dubbed the NCI-DREAM Drug Sensitivity Prediction Challenge, focuses on using genomic information to build models that can estimate the sensitivity of cancer cell lines to a set of small-molecule compounds — both alone and in combination.

The goal is to understand how well computational analysis of -omics data —including proteomics data, SNP data, gene expression data, and drug dose response data — can be used to predict drug activity in cell lines, and ultimately to select the best treatments for patients based on genetic profiling of tumors, Stolovitzky explained.

This challenge is being organized in conjunction with the NCI, which will support the subsequent experimental validation and development of the top performing methods in this category.

Additionally, the best performing team will have the opportunity to publish its results in Nature Biotechnology.

The second challenge for the year is being organized with Prize4Life and calls for methods that can predict the future progression of ALS.

This challenge is intended to try to understand the cause of the disease and its expected progression early on in its development, and to figure out what drugs would work best in each patient's case, Stolovitzky said.

Participants in this category will have access to anonymized data from patients who are currently involved in ALS clinical trials and have given consent for their information to be used in the challenge, he said.

Prize4Life is offering a $25,000 prize for the winning submission in this category.

The third challenge, created in collaboration with Sage Bionetworks, aims to develop algorithms for predicting breast cancer survival. The best performer in this category will have a paper published in Science Translational Medicine.

The final challenge for DREAM 7 focuses on network topology and parameter inference. Participants are expected to develop optimization methods that accurately estimate parameters, predict outcomes of perturbations, and rewire networks in systems biology network models.

This challenge is meant to help researchers "understand how to do experimental design when it comes to reconstruction of gene regulatory networks and understand how to create mathematical models, including what parameters to use," Stolovitzky said.

Although the DREAM organizers will have "a central role" in judging the submissions, Stolovitzky said that the journals who have agreed to publish the fruits from some of the challenge categories — Nature Biotech and Science Translational Medicine — will also provide "challenge-assisted peer review."

That means that the journals will take into account the participants' performance in the challenge during the publication review process so that the papers that result from participation in DREAM have the "highest standards," Stolovitzky said.

DREAM is also partnering with Open Network Biology — a new open access journal published by BioMed Central — which has agreed to publish the best performing methods following the peer-review process. ONB has also agreed to waive its per-article processing charge of £1200 ($1,868) to encourage participation.

While the timelines haven't yet been finalized, it's likely that most submissions will be due by mid-October although entries for some challenges could be due as early as Oct. 1, Stolovitzky said.

The winning entries from each challenge will be presented at the DREAM 7 conference, which will be held in San Francisco on Nov. 12-14.

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